In a funny way, by dusty metaphysics I actually meant the great Swiss philosopher Friedrich Nietzsche.
In Genealogy of Morals he has quotes such as "Science is not nearly independent…, in every respect it first needs a value-ideal, value-creating power, in whose service it can believe in itself,—science itself never creates values." [1] using the word wissenschaft for science, knowledge-making, translating literally the German word. The point was that we are already beyond any dreams Nietzsche could have imagined, the dichotomy religion/science was merely a cultural artefact of the Enlightenment. Hence the replacement you mention is not even an issue.
As for "hardly knowing anything", just looking at the front page of HN right now: we are discovering new water sources on the Moon [2], new primitive cells [3]. We are improving, however knowledge is not about totality (omni-scientia, as the religious terminology would put it). Even if we were to condense all the knowledge in one place, hoard it, it would only collapse into a black hole, our universe is rather limited. Knowledge is about principles: we will never again have to worry about the sun not rising tomorrow because we made the god of Sun angry (although we should worry that the Sun will evaporate Earth in a few billion years, so I suppose Nietzsche has his point [4]).
[1] Two Genealogies of Human Values: Nietzsche Versus Edward O. Wilson on the Consilience of Philosophy, Science and Technology, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978441
[2] https://news.ycombinator.com/item?id=35565553
[3] https://news.ycombinator.com/item?id=35537248
[4] 'Once upon a time, in some out of the way corner of that universe which is dispersed into numberless twinkling solar systems, there was a star upon which clever beasts invented knowing. That was the most arrogant and mendacious minute of "world history," but nevertheless, it was only a minute. After nature had drawn a few breaths, the star cooled and congealed, and the clever beasts had to die.', 1873, F. Nietzsche, On Truth and Lies in a Nonmoral Sense